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About

the

cover:

DNA transcription

by

nRNA.

Colored

transmission electron micrograph

of DNA and

messenger

RNA

(mRNA)

molecules

forming

a feather-like,

transcriptionally

active

structure. This DNA is from

the nucleus

of an

amphibian

egg.

The

backbone

of the feather, running

down the image,

is a long strand

of DNA coated

with

protein.

Numerous nRNA

molecules

extend in clusters

from the DNA

strand. Transcription

of

genetic

information

begins

at

one end

of the

gene,

with the mRNA

molecules

growing

longer

as they approach completion.

Tfanscription

is the first

step in

protein

synthesis.

Magnification:

approximately x30,000.

Li

brary of

Con

gress

Catatogi ng-i

n

-

Publication

Data

Lewin,

Benjamin.

Genes

IX / Benjamin

Lewin.

P';

cm'

Includes

bibliographical

references

and index.

ISBN-

I

3: 97 8-0-7

637

-406)-4

(alk.

paper)

ISBN-

l0:

0-7 637

-4063-2

l.

Genetics. 2.

Genes.

I. Title.

II. Tirle:

Genes 9. III. Title:

Genes nine.

[DNLM:

l.

Genes-physiology.

2.

DNA-genetics.

3.

Genetic Processes. 4.

Genome. 5. Proteins-genetics.

6. RNA-genetics.

QU

470 L672g20061

QH430.L4

2006

576.5-dc22

20060t0787

6048

Printed

in

the United

States

of America

rr

I0 09

08 07

l0 9

8 7 6 5 43

2 |

Brief

Contents

vi

Preface

xvi

408

428

@

(D

Q

C.n.,

nre DNn L

@

C.n., Code

for Proteins

23

@

rn.

rnrerrupreo

Gene

17

@

ff.r.

Content of the Genome 55

@

C.nore Sequences and

Gene

Numbers 76

@

Ctusters and Repeats 98

@

u.rr.nger RNA 1.27

@

erotein Synthesis 1,51.

@

Uting the Genetic Code

189

@

Protein

Localization

21.8

@

Tr.nrrription 256

@

rh. 0peron 3oo

@

negutatory RNA 331

@

ef,rg. Strategies 34g

@

rf.r. Repticon 376

@

*tractrromosomal

Replicons 3gz

@

aacterial

Repl.ication

Is Connected

to

the Cett

Cycle

@

or,rn Replication

@

Homotogous

and Site-Specific

Recombination

457

@

nepair

Systems

4gg

@rt.ntposons

521.

@

R.trouiruses

and

Retroposons

550

@

trrrne

Diversity 570

Glossary

845

Index

867

Promoters

and

Enhancers

609

Activating

Transcription

640

RNA

Spl.icing

and

Processing

667

Catatytic

RNA

706

Chromosomes

729

Nucleosomes

757

ControL[ing

Chromatin

Structure

796

Epigenetic

Effects

Are

Inherited

818

Contents

Preface xvi

1

Genes Are

DNA

1,

Introduction

2

DNA

Is

the Genetic

Material

of Bacteria

3

DNA

Is

the Genetic

Material

of Viruses

4

DNA

Is the

Genetic Material

of Animal

Ce[[s 5

IEl

Polynucteotide

Chains Have Nitrogenous

Bases

Linked

to a

Sugar-Phosphate

Backbone

6

DNA Is

a Doubte

Hetix

6

DNA Replication

Is Semiconservative

8

DNA

Strands

Separate

at

the Replication Fork

9

Genetic Information

Can Be Provided

by DNA or RNA

10

Nucteic

Acids

Hybridize

by Base

Pairing

1,2

Mutations

Change

the Sequence

of DNA

1.4

Mutations

May

Affect

Single Base

Pairs

or

Longer

Sequences

75

The

Effects

of

Mutations

Can Be

Reversed 76

Mutations

Are

Concentrated

at

Hotspots

Il

Many

Hotspots

Result

from Modified

Bases

18

Some Hereditary

Agents

Are

Extremety

Smatl 79

Summary

20

2

Genes

Code

for

Proteins

23

Introduction

24

A Gene

Codes for

a

Single Polypeptide

24

Mutations

in

the

Same

Gene Cannot

Complement

25

Mutations

May

Cause Loss-of-Function

or

Gain-of-Function

26

A Locus

May

Have

Many Different

Mutant Alleles

Zl

A Locus May

Have

More

than

One Witd-type

Altete

28

Recombination

0ccurs

by Physicat

Exchange

of DNA

28

The

Genetic

Code Is Triptet

30

Every

Sequence

Has

Three Possibte

Reading Frames

3l

Prokaryotic

Genes

Are

Colinear

with Their Proteins

32

vi

3

Several

Processes

Are Required

to

Express

the

Protein

Product

of a Gene 33

Proteins Are Trans-acting,

but Sites on DNA

Are

Crs-acting 35

Summary

36

The

Interrupted

Gene

37

Introduction

38

An

InterruDted

Gene Consists of Exons

and Introns

38

Restriction Endonucteases

Are a Key Too[

in Mapping

DNA

39

0rganization

of

Interrupted

Genes May

Be Conserved

40

Exon Sequences Are

Conserved

but

Introns

Vary

42

Genes Show

a Wide Distribution

of Sizes

43

Some DNA

Sequences Code for More Than

One

Protein

45

How

Did interrupted

Genes Evolve?

47

Some Exons Can Be Equated

with Protein

Functions

49

The Members

of a Gene Famity Have

a

Common

0rganization

51.

Is A[[

Genetic

Information

Contained in DNA?

53

Summary 53

4 The

Content

of the

Genome

55

Introduction

56

Genomes

Can

Be Mapped

by

Linkage,

Restriction

Cteavage,

or

DNA

Sequence

56

IndividuaI

Genomes Show Extensive

Variation

5l

RFLPs

and SNPs

Can

Be

Used for

Genetic Mapping

58

Why Are

Genomes So Large?

60

Eukaryotic

Genomes

Contain Both Nonrepetitive

and Repetitive DNA

Sequences

61,

Genes Can Be Iso[ated

by

the Conservation

of Exons

63

The

Conservation

of Genome

0rganization Hetps

to Identify

Genes

65

0rganettes Have DNA

67

0rganelte Genomes

Are

Circutar DNAs That

Code

for

Organelte Proteins 69

Mitochondrial

DNA 0rganization ]s Variabte 70

The

Chtoroptast Genome

Codes

for Many Proteins

and RNAs

71,

Mitochondria Evolved

by Endosymbiosis 72

Summarv 73

5 Genome Sequences and

Gene

Numbers 76

Introduction 77

Bacterial Gene Numbers Range

0ver an 0rder

of

Magnitude 77

Total

Gene

Number

Is Known for Several Eukaryotes

How Many Different

Types of Genes Are There? 81

The Human

Genome

Has

Fewer Genes Than Expected

How Are

Genes and 0ther Sequences

Distributed

in the Genome? 85

The Y Chromosome Has

SeveraI

Male-Specific

Genes

More Complex Species Evotve

by

Adding New

Gene

Functions

87

How Many

Genes

Are Essential?

89

Genes

Are Expressed

at Widety

Differing Levels

92

How Many

Genes Are Expressed? 93

Expressed

Gene Number Can Be Measured En

Mosse

93

Summarv 94

6 Clusters and Repeats 98

Introduction

99

Gene

Duptication Is

a

Major Force in Evotution 100

Globin Ctusters

Are Formed

by

Duplication

and

Divergence 101

Sequence Divergence Is the Basis

for

the

Evolutionary

Clock

104

The Rate

of

Neutral

Substitution Can

Be Measured

from Divergence

of Repeated Sequences

1.07

Pseudogenes Are Dead Ends

of

Evolution 108

UnequaI

Crossing-over Rearranges Gene Ctusters

109

Genes

for rRNA Form Tandem Repeats 1.1.2

The Reoeated Genes for rRNA Maintain Constant

Sequence

71,4

Crossover

Fixation

Coutd

Maintain IdenticaI Repeats

775

Satettite

DNAs

0ften

Lie in Heterochromatin 1.17

79

83

86

Arthropod Satetlites

Have Very

Short

IdenticaI

Reoeats

1.1.9

Mammalian

Satetlites

Consist of

Hierarchical

Repeats

1.20

Minisate[lites

Are Useful

for Genetic

Mapping

1'23

Summary

725

7

Messenger

RNA

1'27

Introduction

1,28

mRNA

Is Produced by

Transcription

and

Is

Trans[ated

1,29

Transfer RNA

Forms a Ctoverleaf

130

The Acceptor

Stem and

Anticodon

Are at

Ends

of the

Tertiary Structure

1,31,

Messenger

RNA

Is Transtated

by Ribosomes

1'32

Many

Ribosomes

Bind to One

mRNA

133

The

Life Cycte of

Bacterial

Messenger

RNA

135

Eukaryotic

mRNA Is

Modified

During or after

Its

Transcriotion

1'37

The 5'End

of

Eukaryotic

mRNA Is Capped

138

The 3'Terminus

Is Po[yadenytated

739

BacteriaI

mRNA

Degradation

Involves

Multip[e

Enzymes

1.40

mRNA StabiLity

Depends

on

Its Structure

and Sequence

1,41,

mRNA Degradation

Involves

Multipte

Activities

743

Nonsense

Mutations

Trigger a Surveiltance

System

1'44

Eukaryotic

RNAs

Are Transported

745

mRNA Can

Be Specifically

Localized

1'46

Summary

1.47

I

Protein

Synthesis

15L

Introduction

1'52

Protein

Synthesis

0ccurs

by

Initiation,

Etongation,

and

Termination

1'53

SpeciaI

Mechanisms

Control

the

Accuracy

of Protein

Synthesis

156

Initiation

in Bacteria

Needs 30S

Subunits

and

Accessory

Factors

1.57

A SpeciaI

Initiator

tRNA

Starts the

Potypeptide

Chain

158

Use

of

fMet-tRNAt

Is Controlted

by

IF-2 and the

Ribosome

160

Initiation

Involves

Base

Pairing

Between

mRNA

and

rRNA

1.61.

Contents

vii

Sma[[

Subunits

Scan for Initiation

Sites

on

Eukarvotic

mRNA

1,62

Eukaryotes

Use a Comptex

of Many Initiation

Factors

!64

Elongation

Factor

Tu Loads

Aminoacyt-tRNA

into

the A

Site 167

The

Potypeptide

Chain Is Transferred

to Aminoacyl-tRNA

168

Transtocation

Moves

the Ribosome 769

Etongation

Factors

Bind Atternately

to the

Ribosome

170

Three

Codons Terminate

Protein

Synthesis 772

Termination

Codons Are

Recognized

by Protein

Factors

173

RibosomaI

RNA Pervades

Both

RibosomaI

Subunits 775

G:t

Ribosomes

Have

Several Active

Centers 177

165 rRNA

Ptays

an Active

Role in Protein

Synthesis 179

23S rRNA

Has Peptidyl

Transferase

Activity 792

RibosomaI

Structures

Chanqe When

the Subunits

Come

Together

183

Summary

183

I Using

the

Genetic

Code

189

Introduction

190

Represent

Related Amino

Acids

190

Codon-Anticodon

Recognition

Invotves

Wobbting

1.92

tRNAs Are Processed

from

Longer Precursors

lg4

IRNA Contains

Modified

Bases

1,94

Modified

Bases

Affect

Anticodon-Codon

Pairing

796

There

Are

Sporadic

Alterations

of the

Universa[

Code 1.97

Novel

Amino

Acids

Can Be Inserted

at Certain

Stop

Codons

799

tRNAs Are

Charged

with Amino

Acids

by Synthetases

200

Aminoacyt-tRNA

Synthetases

Fat[

into Two

Groups

ZO1,

Synthetases

Use Proofreading

to Improve

Accuracy

203

Suppressor

tRNAs

Have

Mutated

Anticodons

That

Read

New

Codons

206

There

Are Nonsense

Suppressors

for

Each Termination

Codon 207

Suppressors

May

Compete

with

Witd-Type

Reading

of the Code

208

The

Ribosome

Inftuences

the Accuracy

of Translation

209

Recoding

Changes Codon Meanings 21.7

Frameshifting

0ccurs at Stippery

Sequences 21,3

Bypassing Involves

Ribosome Movement 274

Summary 215

10 Protein

Localization

21,8

Introduction

220

Passage

Across a Membrane

Requires a Special

Apparatus

220

Protein

Transtocation May

Be Posttranstational

or Cotranslationa[ 227

Chaperones May

Be Required for Protein

Folding

223

Chaperones

Are

Needed

by

Newty

Synthesized

and by

Denatured

Proteins 224

The Hsp70

Famity Is

Ubiquitous 226

SignaI Sequences Initiate

Translocation

227

The

Signal

Sequence Interacts with

the SRP 228

The

SRP Interacts

with the SRP Receptor

229

The Translocon

Forms

a

Pore

231,

Transtocation

Requires Insertion

into

the Transtocon

and

(Sometimes)

a Ratchet in

the ER 233

Reverse Translocation

Sends

Proteins

to

the CvtosoI

for Degradation

234

Proteins Reside in

Membranes

by

Means

of

Hydrophobic

Regions 235

Anchor

Sequences Determine

Protein

0rientation

236

How Do Proteins

Insert into

Membranes?

238

PosttranstationaI

Membrane Insertion

Depends

on Leader

Sequences 240

A Hierarchy

of Sequences Determines

Location

within

0rgane[[es 247

Inner

and Outer MitochondriaI

Membranes

Have

Different

Transtocons

243

Peroxisomes

Employ

Another

Type

of

Translocation

System 245

Bacteria

Use

Both

CotranslationaI

and Posttranstationa[

Trans[ocation

246

The Sec

System Transports Proteins

into

and Through

the Inner Membrane

247

Sec-Independent

Transtocation

Systems in

E.

coLi 249

Summary

250

viii

Contents

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L,

Antisense

RNA

Can Be Used

to Inactivate

Gene

Exoression

338

Smatl. RNA Motecules

Can Regutate Trans[ation

339

Bacteria

Contain

Regulator

RNAs

341,

MicroRNAs

Are

Regulators

in Many

Eukaryotes

342

RNA Interference

Is Related

to

Gene Silencinq

343

Summary

345

14 Phage

Strategies

349

Introduction

350

Lytic Devetopment

Is Divided

into Two Periods

352

Lytic

Devetopment

Is Controtled

by

a Cascade

353

Two

Types

of Regutatory

Event

Control

the Lytic

Cascade

354

The

T7

and T4

Genomes

Show Functiona[

Clustering 355

Lambda

Immediate

Earty

and Detayed

Earty Genes Are

Needed

for

Both

Lysogeny

and

the Lytic

Cycle 356

The Lytic

Cycte Depends

on Antitermination

357

Lysogeny

Is Maintained

by Repressor

Protein

359

The Repressor

and Its

0perators Define

the

Immunity

Region

360

The

DNA-Binding

Form

of Repressor

Is

a

Dimer

361

Repressor

Uses

a

Helix-Turn-Helix

Motif

to Bind

DNA

362

The

Recognition

Helix Determines

Specificity

for

DNA

363

Repressor Dimers

Bind

Cooperativety

to the

Operator

364

Repressor

at

0*2 Interacts

with

RNA Potymerase

at P*,

365

Repressor

Maintains

an Autogenous

Circuit

366

Cooperative

Interactions

Increase

the Sensitivitv

of Regulation

367

The

cil

and cIIi

Genes

Are Needed

to Establish

Lysogeny

368

A Poor

Promoter

Requires

cII Protein

369

Lysogeny

Requires

SeveraI Events

369

The

cro

Repressor

Is Needed

for

Lytic Infection

311.

What Determines

the Balance

Between

Lysogeny

and

the Lytic

Cycte?

373

Summary

374

15 The

Replicon 376

Introduction

377

Replicons

Can

Be

Linear or Circutar

378

0rigins Can Be Mapped

by

Autoradiography

and Electrophoresis

379

Does Methytation

at the

Origin Regulate Initiation?

380

Origins May Be

Sequestered

after Reptication

381

Each Eukaryotic

Chromosome

Contains Many

Repticons

383

Reptication

0rigins Can Be Isolated in Yeast

384

Licensing

Factor

Controts Eukaryotic Rerep[ication

385

Licensing Factor

Consists

of

MCM Proteins

386

D Loops Maintain

Mitochondrial

0rigins

388

Summary 389

16 Extrachromosomal

Repticons

392

Introduction

393

The Ends

of Linear DNA Are

a

Prob[em

for

Reptication

393

Termina[ Proteins

Enabte Initiation

at the Ends

of ViraI DNAs

394

Rol.ting Circles Produce

Muttimers

of a Replicon

396

Rotting

Circtes Are

Used to Repticate Phage

Genomes

397

The F

Plasmid Is Transferred

by Conjugation

between

Bacteria

398

Conjugation Transfers

Single-Stranded

DNA

400

The Bacterial

Ti Ptasmid

Causes

Crown Ga[[ Disease

in Ptants

401.

T-DNA

Carries Genes Required for

Infection

402

Transfer

of T-DNA

Resembtes Bacteria[

Conjugation

405

Summary 407

17

Bacterial

Replication

Is

Connected

to

the CeLL

CycLe408

Introduction

409

Reptication Is

Connected

to the Ce[[

Cycte

410

The

Septum Divides

a

Bacterium

into Progeny

That

Each

Contain

a Chromosome

41,7

Mutations

in Division

or Segregation Affect

Ce[[

Shaoe 41,2

FtsZ Is Necessary

for

Septum Formation

413

mrn Genes

Regulate

the Location

of the

Septum

475

Contents

Lewin Benjamin (ed.) Genes IX

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